src/gromacs/gmxlib/nonbonded/nb_generic_cg.c

   1 /*
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   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 #include "gmxpre.h"
  38
  39 #include "config.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/legacyheaders/types/simple.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/legacyheaders/typedefs.h"
  46 #include "nb_generic_cg.h"
  47 #include "gromacs/legacyheaders/nonbonded.h"
  48 #include "nb_kernel.h"
  49 #include "gromacs/legacyheaders/nrnb.h"
  50
  51 #include "gromacs/utility/fatalerror.h"
  52
  53 void
  54 gmx_nb_generic_cg_kernel(t_nblist *                nlist,
  55                          rvec *                    xx,
  56                          rvec *                    ff,
  57                          t_forcerec *              fr,
  58                          t_mdatoms *               mdatoms,
  59                          nb_kernel_data_t *        kernel_data,
  60                          t_nrnb *                  nrnb)
  61 {
  62     int           nri, ntype, table_nelements, ielec, ivdw;
  63     real          facel, gbtabscale;
  64     int           n, is3, i3, k, nj0, nj1, j3, ggid, nnn, n0;
  65     int           ai0, ai1, ai, aj0, aj1, aj;
  66     real          shX, shY, shZ;
  67     real          fscal, tx, ty, tz;
  68     real          rinvsq;
  69     real          iq;
  70     real          qq, vcoul, krsq, vctot;
  71     int           nti, nvdwparam;
  72     int           tj;
  73     real          rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR;
  74     real          rinvsix;
  75     real          Vvdwtot;
  76     real          Vvdw_rep, Vvdw_disp;
  77     real          ix, iy, iz, fix, fiy, fiz;
  78     real          jx, jy, jz;
  79     real          dx, dy, dz, rsq, rinv;
  80     real          c6, c12, cexp1, cexp2, br;
  81     real *        charge;
  82     real *        shiftvec;
  83     real *        vdwparam;
  84     int *         shift;
  85     int *         type;
  86     t_excl *      excl;
  87     real *        fshift;
  88     real *        Vc;
  89     real *        Vvdw;
  90     real          tabscale;
  91     real *        VFtab;
  92     real *        x;
  93     real *        f;
  94
  95     x                   = xx[0];
  96     f                   = ff[0];
  97     ielec               = nlist->ielec;
  98     ivdw                = nlist->ivdw;
  99
 100     fshift              = fr->fshift[0];
 101     Vc                  = kernel_data->energygrp_elec;
 102     Vvdw                = kernel_data->energygrp_vdw;
 103     tabscale            = kernel_data->table_elec_vdw->scale;
 104     VFtab               = kernel_data->table_elec_vdw->data;
 105
 106     /* avoid compiler warnings for cases that cannot happen */
 107     nnn                 = 0;
 108     vcoul               = 0.0;
 109     eps                 = 0.0;
 110     eps2                = 0.0;
 111
 112     /* 3 VdW parameters for buckingham, otherwise 2 */
 113     nvdwparam           = (nlist->ivdw == 2) ? 3 : 2;
 114     table_nelements     = (ielec == 3) ? 4 : 0;
 115     table_nelements    += (ivdw == 3) ? 8 : 0;
 116
 117     charge              = mdatoms->chargeA;
 118     type                = mdatoms->typeA;
 119     facel               = fr->epsfac;
 120     shiftvec            = fr->shift_vec[0];
 121     vdwparam            = fr->nbfp;
 122     ntype               = fr->ntype;
 123
 124     for (n = 0; (n < nlist->nri); n++)
 125     {
 126         is3              = 3*nlist->shift[n];
 127         shX              = shiftvec[is3];
 128         shY              = shiftvec[is3+1];
 129         shZ              = shiftvec[is3+2];
 130         nj0              = nlist->jindex[n];
 131         nj1              = nlist->jindex[n+1];
 132         ai0              = nlist->iinr[n];
 133         ai1              = nlist->iinr_end[n];
 134         vctot            = 0;
 135         Vvdwtot          = 0;
 136         fix              = 0;
 137         fiy              = 0;
 138         fiz              = 0;
 139
 140         for (k = nj0; (k < nj1); k++)
 141         {
 142             aj0              = nlist->jjnr[k];
 143             aj1              = nlist->jjnr_end[k];
 144             excl             = &nlist->excl[k*MAX_CGCGSIZE];
 145
 146             for (ai = ai0; (ai < ai1); ai++)
 147             {
 148                 i3               = ai*3;
 149                 ix               = shX + x[i3+0];
 150                 iy               = shY + x[i3+1];
 151                 iz               = shZ + x[i3+2];
 152                 iq               = facel*charge[ai];
 153                 nti              = nvdwparam*ntype*type[ai];
 154
 155                 /* Note that this code currently calculates
 156                  * all LJ and Coulomb interactions,
 157                  * even if the LJ parameters or charges are zero.
 158                  * If required, this can be optimized.
 159                  */
 160
 161                 for (aj = aj0; (aj < aj1); aj++)
 162                 {
 163                     /* Check if this interaction is excluded */
 164                     if (excl[aj-aj0] & (1<<(ai-ai0)))
 165                     {
 166                         continue;
 167                     }
 168
 169                     j3               = aj*3;
 170                     jx               = x[j3+0];
 171                     jy               = x[j3+1];
 172                     jz               = x[j3+2];
 173                     dx               = ix - jx;
 174                     dy               = iy - jy;
 175                     dz               = iz - jz;
 176                     rsq              = dx*dx+dy*dy+dz*dz;
 177                     rinv             = gmx_invsqrt(rsq);
 178                     rinvsq           = rinv*rinv;
 179                     fscal            = 0;
 180
 181                     if (ielec == 3 || ivdw == 3)
 182                     {
 183                         r                = rsq*rinv;
 184                         rt               = r*tabscale;
 185                         n0               = rt;
 186                         eps              = rt-n0;
 187                         eps2             = eps*eps;
 188                         nnn              = table_nelements*n0;
 189                     }
 190
 191                     /* Coulomb interaction. ielec==0 means no interaction */
 192                     if (ielec > 0)
 193                     {
 194                         qq               = iq*charge[aj];
 195
 196                         switch (ielec)
 197                         {
 198                             case 1:
 199                                 /* Vanilla cutoff coulomb */
 200                                 vcoul            = qq*rinv;
 201                                 fscal            = vcoul*rinvsq;
 202                                 break;
 203
 204                             case 2:
 205                                 /* Reaction-field */
 206                                 krsq             = fr->k_rf*rsq;
 207                                 vcoul            = qq*(rinv+krsq-fr->c_rf);
 208                                 fscal            = qq*(rinv-2.0*krsq)*rinvsq;
 209                                 break;
 210
 211                             case 3:
 212                                 /* Tabulated coulomb */
 213                                 Y                = VFtab[nnn];
 214                                 F                = VFtab[nnn+1];
 215                                 Geps             = eps*VFtab[nnn+2];
 216                                 Heps2            = eps2*VFtab[nnn+3];
 217                                 nnn             += 4;
 218                                 Fp               = F+Geps+Heps2;
 219                                 VV               = Y+eps*Fp;
 220                                 FF               = Fp+Geps+2.0*Heps2;
 221                                 vcoul            = qq*VV;
 222                                 fscal            = -qq*FF*tabscale*rinv;
 223                                 break;
 224
 225                             case 4:
 226                                 /* GB */
 227                                 gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 228                                 break;
 229
 230                             default:
 231                                 gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 232                                 break;
 233                         }
 234                         vctot            = vctot+vcoul;
 235                     }  /* End of coulomb interactions */
 236
 237
 238                     /* VdW interaction. ivdw==0 means no interaction */
 239                     if (ivdw > 0)
 240                     {
 241                         tj               = nti+nvdwparam*type[aj];
 242
 243                         switch (ivdw)
 244                         {
 245                             case 1:
 246                                 /* Vanilla Lennard-Jones cutoff */
 247                                 c6               = vdwparam[tj];
 248                                 c12              = vdwparam[tj+1];
 249
 250                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 251                                 Vvdw_disp        = c6*rinvsix;
 252                                 Vvdw_rep         = c12*rinvsix*rinvsix;
 253                                 fscal           += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 254                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 255                                 break;
 256
 257                             case 2:
 258                                 /* Buckingham */
 259                                 c6               = vdwparam[tj];
 260                                 cexp1            = vdwparam[tj+1];
 261                                 cexp2            = vdwparam[tj+2];
 262
 263                                 rinvsix          = rinvsq*rinvsq*rinvsq;
 264                                 Vvdw_disp        = c6*rinvsix;
 265                                 br               = cexp2*rsq*rinv;
 266                                 Vvdw_rep         = cexp1*exp(-br);
 267                                 fscal           += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
 268                                 Vvdwtot          = Vvdwtot+Vvdw_rep-Vvdw_disp;
 269                                 break;
 270
 271                             case 3:
 272                                 /* Tabulated VdW */
 273                                 c6               = vdwparam[tj];
 274                                 c12              = vdwparam[tj+1];
 275
 276                                 Y                = VFtab[nnn];
 277                                 F                = VFtab[nnn+1];
 278                                 Geps             = eps*VFtab[nnn+2];
 279                                 Heps2            = eps2*VFtab[nnn+3];
 280                                 Fp               = F+Geps+Heps2;
 281                                 VV               = Y+eps*Fp;
 282                                 FF               = Fp+Geps+2.0*Heps2;
 283                                 Vvdw_disp        = c6*VV;
 284                                 fijD             = c6*FF;
 285                                 nnn             += 4;
 286                                 Y                = VFtab[nnn];
 287                                 F                = VFtab[nnn+1];
 288                                 Geps             = eps*VFtab[nnn+2];
 289                                 Heps2            = eps2*VFtab[nnn+3];
 290                                 Fp               = F+Geps+Heps2;
 291                                 VV               = Y+eps*Fp;
 292                                 FF               = Fp+Geps+2.0*Heps2;
 293                                 Vvdw_rep         = c12*VV;
 294                                 fijR             = c12*FF;
 295                                 fscal           += -(fijD+fijR)*tabscale*rinv;
 296                                 Vvdwtot          = Vvdwtot + Vvdw_disp + Vvdw_rep;
 297                                 break;
 298
 299                             default:
 300                                 gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 301                                 break;
 302                         }
 303                     }  /* end VdW interactions */
 304
 305
 306                     tx               = fscal*dx;
 307                     ty               = fscal*dy;
 308                     tz               = fscal*dz;
 309                     f[i3+0]         += tx;
 310                     f[i3+1]         += ty;
 311                     f[i3+2]         += tz;
 312                     f[j3+0]         -= tx;
 313                     f[j3+1]         -= ty;
 314                     f[j3+2]         -= tz;
 315                     fix             += tx;
 316                     fiy             += ty;
 317                     fiz             += tz;
 318                 }
 319             }
 320         }
 321
 322         fshift[is3]     += fix;
 323         fshift[is3+1]   += fiy;
 324         fshift[is3+2]   += fiz;
 325         ggid             = nlist->gid[n];
 326         Vc[ggid]        += vctot;
 327         Vvdw[ggid]      += Vvdwtot;
 328     }
 329     /* Estimate flops, average for generic cg kernel:
 330      * 12  flops per outer iteration
 331      * 100 flops per inner iteration
 332      */
 333     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_CG, nlist->nri*12 + nlist->jindex[n]*100);
 334 }